Challenges and prospects in genome-wide quantitative trait loci mapping of standing genetic variation in natural populations
Schielzeth H, Husby A (2014)
Annals of the New York Academy of Sciences 1320(1): 35-57.
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Autor*in
Schielzeth, HolgerUniBi ;
Husby, Arild
Einrichtung
Abstract / Bemerkung
A considerable challenge in evolutionary genetics is to understand the genetic mechanisms that facilitate or impede
evolutionary adaptation in natural populations. For this, we must understand the genetic loci contributing to trait
variation and the selective forces acting on them. The decreased costs and increased feasibility of obtaining genotypic data on a large number of individuals have greatly facilitated gene mapping in natural populations, particularly because organisms whose genetics have been historically difficult to study are now within reach. Here we review the methods available to evolutionary ecologists interested in dissecting the genetic basis of traits in natural populations. Our focus lies on standing genetic variation in outbred populations. We present an overview of the current state of research in the field, covering studies on both plants and animals. We also draw attention to particular challenges associated with the discovery of quantitative trait loci and discuss parallels to studies on crops, livestock, and humans. Finally, we point to some likely future developments in genetic mapping studies.
Stichworte
genetic architecture;
genotype–phenotype map;
pedigreed wild populations;
quantitative trait loci;
complex trait analysis;
standing genetic variation
Erscheinungsjahr
2014
Zeitschriftentitel
Annals of the New York Academy of Sciences
Band
1320
Ausgabe
1
Seite(n)
35-57
ISSN
0077-8923
Page URI
https://pub.uni-bielefeld.de/record/2692649
Zitieren
Schielzeth H, Husby A. Challenges and prospects in genome-wide quantitative trait loci mapping of standing genetic variation in natural populations. Annals of the New York Academy of Sciences. 2014;1320(1):35-57.
Schielzeth, H., & Husby, A. (2014). Challenges and prospects in genome-wide quantitative trait loci mapping of standing genetic variation in natural populations. Annals of the New York Academy of Sciences, 1320(1), 35-57. doi:10.1111/nyas.12397
Schielzeth, Holger, and Husby, Arild. 2014. “Challenges and prospects in genome-wide quantitative trait loci mapping of standing genetic variation in natural populations”. Annals of the New York Academy of Sciences 1320 (1): 35-57.
Schielzeth, H., and Husby, A. (2014). Challenges and prospects in genome-wide quantitative trait loci mapping of standing genetic variation in natural populations. Annals of the New York Academy of Sciences 1320, 35-57.
Schielzeth, H., & Husby, A., 2014. Challenges and prospects in genome-wide quantitative trait loci mapping of standing genetic variation in natural populations. Annals of the New York Academy of Sciences, 1320(1), p 35-57.
H. Schielzeth and A. Husby, “Challenges and prospects in genome-wide quantitative trait loci mapping of standing genetic variation in natural populations”, Annals of the New York Academy of Sciences, vol. 1320, 2014, pp. 35-57.
Schielzeth, H., Husby, A.: Challenges and prospects in genome-wide quantitative trait loci mapping of standing genetic variation in natural populations. Annals of the New York Academy of Sciences. 1320, 35-57 (2014).
Schielzeth, Holger, and Husby, Arild. “Challenges and prospects in genome-wide quantitative trait loci mapping of standing genetic variation in natural populations”. Annals of the New York Academy of Sciences 1320.1 (2014): 35-57.
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Ecological genomics of Boechera stricta: identification of a QTL controlling the allocation of methionine- vs branched-chain amino acid-derived glucosinolates and levels of insect herbivory.
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Moritz, Plant Biol. 3(), 2001
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Hawthorne DJ, Via S., Nature 412(6850), 2001
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The genetic architecture of parallel armor plate reduction in threespine sticklebacks
Colosimo, PLoS Biol. 2(), 2004
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Composite interval mapping reveals a major locus influencing embryonic development rate in rainbow trout (Oncorhynchus mykiss).
Robison BD, Wheeler PA, Sundin K, Sikka P, Thorgaard GH., J. Hered. 92(1), 2001
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Hecht, Genes Genom. Genet. 2(), 2012
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Borowsky R, Wilkens H., J. Hered. 93(1), 2002
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Protas M, Tabansky I, Conrad M, Gross JB, Vidal O, Tabin CJ, Borowsky R., Evol. Dev. 10(2), 2008
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Gross JB, Borowsky R, Tabin CJ., PLoS Genet. 5(1), 2009
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O'Quin KE, Yoshizawa M, Doshi P, Jeffery WR., PLoS ONE 8(2), 2013
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Mapping of quantitative trait loci controlling adaptive traits in coastal Douglas-fir. I. Timing of vegetative bud flush.
Jermstad KD, Bassoni DL, Jech KS, Wheeler NC, Neale DB., Theor. Appl. Genet. 102(8), 2001
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Mapping of quantitative trait loci controlling adaptive traits in coastal Douglas-fir. II. Spring and fall cold-hardiness.
Jermstad KD, Bassoni DL, Wheeler NC, Anekonda TS, Aitken SN, Adams WT, Neale DB., Theor. Appl. Genet. 102(8), 2001
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Mapping of quantitative trait loci controlling adaptive traits in coastal Douglas fir. III. Quantitative trait loci-by-environment interactions.
Jermstad KD, Bassoni DL, Jech KS, Ritchie GA, Wheeler NC, Neale DB., Genetics 165(3), 2003
PMID: 14668397
Jermstad KD, Bassoni DL, Jech KS, Ritchie GA, Wheeler NC, Neale DB., Genetics 165(3), 2003
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A rare major plant QTL determines non-responsiveness to a gall-forming insect in willow
Höglund, Tree Genet. Genomes 8(), 2012
Höglund, Tree Genet. Genomes 8(), 2012
Few Mendelian genes underlie the quantitative response of a forest tree, Eucalyptus globulus, to a natural fungal epidemic.
Freeman JS, Potts BM, Vaillancourt RE., Genetics 178(1), 2008
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Freeman JS, Potts BM, Vaillancourt RE., Genetics 178(1), 2008
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Distribution of genomic regions differentiating oak species assessed by QTL detection.
Saintagne C, Bodenes C, Barreneche T, Pot D, Plomion C, Kremer A., Heredity (Edinb) 92(1), 2004
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Saintagne C, Bodenes C, Barreneche T, Pot D, Plomion C, Kremer A., Heredity (Edinb) 92(1), 2004
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Quantitative trait loci mapping for vegetative propagation in pedunculate oak
Scotti-Saintagne, Ann. For. Sci 62(), 2005
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A RAPD, AFLP and SSR linkage map, and QTL analysis in European beech (Fagus sylvatica L.).
Scalfi M, Troggio M, Piovani P, Leonardi S, Magnaschi G, Vendramin GG, Menozzi P., Theor. Appl. Genet. 108(3), 2003
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Discovery and application of insertion-deletion (INDEL) polymorphisms for QTL mapping of early life-history traits in Atlantic salmon.
Vasemagi A, Gross R, Palm D, Paaver T, Primmer CR., BMC Genomics 11(), 2010
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Vasemagi A, Gross R, Palm D, Paaver T, Primmer CR., BMC Genomics 11(), 2010
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Quantitative trait loci for body weight, condition factor and age at sexual maturation in Arctic charr (Salvelinus alpinus): comparative analysis with rainbow trout (Oncorhynchus mykiss) and Atlantic salmon (Salmo salar).
Moghadam HK, Poissant J, Fotherby H, Haidle L, Ferguson MM, Danzmann RG., Mol. Genet. Genomics 277(6), 2007
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Genome-wide association genetics of an adaptive trait in lodgepole pine.
Parchman TL, Gompert Z, Mudge J, Schilkey FD, Benkman CW, Buerkle CA., Mol. Ecol. 21(12), 2012
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Parchman TL, Gompert Z, Mudge J, Schilkey FD, Benkman CW, Buerkle CA., Mol. Ecol. 21(12), 2012
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Admixture mapping of male nuptial colour and body shape in a recently formed hybrid population of threespine stickleback.
Malek TB, Boughman JW, Dworkin I, Peichel CL., Mol. Ecol. 21(21), 2012
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A strong quantitative trait locus for wing length on chromosome 2 in a wild population of great reed warblers
Tarka, Proc. R. Soc. B 1692(), 2010
Tarka, Proc. R. Soc. B 1692(), 2010
QTL linkage mapping of wing length in zebra finch using genome-wide SNP markers
Schielzeth, Mol. Ecol. 21(), 2012
Schielzeth, Mol. Ecol. 21(), 2012
Development of a linkage map and mapping of phenotypic polymorphisms in a free-living population of Soay sheep (Ovis aries).
Beraldi D, McRae AF, Gratten J, Slate J, Visscher PM, Pemberton JM., Genetics 173(3), 2006
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Beraldi D, McRae AF, Gratten J, Slate J, Visscher PM, Pemberton JM., Genetics 173(3), 2006
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Quantitative trait loci (QTL) mapping of resistance to strongyles and coccidia in the free-living Soay sheep (Ovis aries).
Beraldi D, McRae AF, Gratten J, Pilkington JG, Slate J, Visscher PM, Pemberton JM., Int. J. Parasitol. 37(1), 2006
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Beraldi D, McRae AF, Gratten J, Pilkington JG, Slate J, Visscher PM, Pemberton JM., Int. J. Parasitol. 37(1), 2006
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Mapping quantitative trait Loci underlying fitness-related traits in a free-living sheep population.
Beraldi D, McRae AF, Gratten J, Slate J, Visscher PM, Pemberton JM., Evolution 61(6), 2007
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Beraldi D, McRae AF, Gratten J, Slate J, Visscher PM, Pemberton JM., Evolution 61(6), 2007
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QTL mapping for sexually dimorphic fitness-related traits in wild bighorn sheep.
Poissant J, Davis CS, Malenfant RM, Hogg JT, Coltman DW., Heredity (Edinb) 108(3), 2011
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Morse AM, Peterson DG, Islam-Faridi MN, Smith KE, Magbanua Z, Garcia SA, Kubisiak TL, Amerson HV, Carlson JE, Nelson CD, Davis JM., PLoS ONE 4(2), 2009
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A widespread chromosomal inversion polymorphism contributes to a major life-history transition, local adaptation, and reproductive isolation
Lowry, PLoS Biol. 8(), 2010
Lowry, PLoS Biol. 8(), 2010
Spatially and temporally varying selection on intrapopulation quantitative trait loci for a life history trade-off in Mimulus guttatus.
Mojica JP, Lee YW, Willis JH, Kelly JK., Mol. Ecol. 21(15), 2012
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Mojica JP, Lee YW, Willis JH, Kelly JK., Mol. Ecol. 21(15), 2012
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Widespread parallel evolution in sticklebacks by repeated fixation of Ectodysplasin alleles.
Colosimo PF, Hosemann KE, Balabhadra S, Villarreal G Jr, Dickson M, Grimwood J, Schmutz J, Myers RM, Schluter D, Kingsley DM., Science 307(5717), 2005
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Colosimo PF, Hosemann KE, Balabhadra S, Villarreal G Jr, Dickson M, Grimwood J, Schmutz J, Myers RM, Schluter D, Kingsley DM., Science 307(5717), 2005
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Environment specific pleiotropy facilitates divergence at the Ectodysplasin locus in threespine stickleback.
Barrett RD, Rogers SM, Schluter D., Evolution 63(11), 2009
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Barrett RD, Rogers SM, Schluter D., Evolution 63(11), 2009
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Avian quantitative genetics
Merilä, Curr. Ornithol. 16(), 2001
Merilä, Curr. Ornithol. 16(), 2001
The design and cross-population application of a genome-wide SNP chip for the great tit Parus major
Bers, Mol. Ecol. Res. 12(), 2012
Bers, Mol. Ecol. Res. 12(), 2012
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Mapping the Horns locus in sheep
Pickering, Proc. Ass. Adv. Anim. Breed. Genet. 18(), 2009
Pickering, Proc. Ass. Adv. Anim. Breed. Genet. 18(), 2009
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